Many genes contain introns that need to be spliced out of newly synthesized messenger RNA precursors (pre-mRNA) to produce mature mRNAs. This process often occurs while pre-mRNAs are still being synthesized by RNA polymerase II, an enzyme responsible for the expression of most eukaryotic genes. The prevalence of such co-transcriptional splicing differs across cell types and developmental stages, yet the mechanisms and functional consequences of this regulation are not well understood.
The RNA-binding protein PTBP1 is a master regulator of pre-mRNA splicing expressed at high levels in proliferating cells and downregulated upon differentiation. The downregulation effect is particularly evident in developing neurons, consistent with the role of PTBP1 in repressing neuron-specific splicing events. In a new study, out now in Molecular Cell, Iannone (now at the Wellcome Trust), Kainov, Zhuravskaya et al. investigated PTBP1’s role in co-transcriptional splicing. The authors, including Fursham Hamid and Eugene Makeyev from the CDN, and Takayuki Nojima from Kyushu University, acutely depleted PTBP1 from mouse embryonic stem cells and then analysed the splicing patterns of RNA polymerase II-associated transcripts.
This revealed hundreds of introns activated by PTBP1 in a co-transcriptional manner, at odds with the better-known function of this protein as a splicing repressor. Interestingly, some co-transcriptionally activated introns are retained in mature mRNAs when PTBP1 is not available. One of the targets of this regulation is the DNMT3B gene encoding an epigenetic factor required for the establishment of normal DNA methylation patterns in early development. Retention of a PTBP1-activated intron in the DNMT3B mRNA interrupts the protein-coding sequence and promotes nonsense-mediated decay of this transcript. Iannone, Kainov, Zhuravskaya et al. show that this mechanism supports the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from aberrant methylation.
In conclusion, this work identifies PTBP1 as an activator of co-transcriptional splicing mediating the epigenetic control of cellular identity.